Codon usage in twelve species of Drosophila.
Codon usage in twelve species of Drosophila.
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DOI：
10.1186/1471-2148-7-226
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发表时间：
2007-11-15
影响因子：
3.4
通讯作者：
Powell JR
中科院分区：
文献类型：
--
作者：
Vicario S;Moriyama EN;Powell JR
密码子使用偏倚（CUB），同义密码子的不均匀使用，是一个普遍存在的观察，几乎所有的生物体检查。密码子使用的模式在密切相关的物种中通常是相似的，但在远亲生物中显著不同，例如，细菌酵母和果蝇对CUB的几种解释已经被提出，有些已经得到了观察和实验的支持，尽管对进化力量（随机漂移，突变偏差和选择）及其相对重要性的彻底理解仍有待确定。最近获得的12种果蝇的完整基因组DNA序列为研究这些问题提供了前所未有的机会。我们在这里报告的密码子使用的12个物种的模式，并提供有关可能的进化力量的见解。(1)密码子的使用在11/12的物种中是相当稳定的：G-和特别是C-末端密码子使用最频繁，因此定义了优选的密码子。(2)在优选密码子中唯一改变的氨基酸是丝氨酸，其中六种黑腹动物偏爱TCC，而其他物种，特别是果蝇亚属物种，偏爱AGC。(3)D. willistoni是这些普遍化的例外，在摆动位置中有7个氨基酸的密码子使用向A/T移动。(4)氨基酸对总体CUB的贡献不同，Leu最大，Asp最小。(5)在二次简并氨基酸中，A/G末端氨基酸比T/C末端氨基酸具有更大的密码子选择性。(6)在不同的染色体臂或元件中，非重组元件F（点染色体）上的基因具有最少的CUB，而元件A（X染色体）上的基因具有最多的CUB。(7)内含子表明所有物种中的突变偏倚约为2：1，AT：GC，与密码子使用偏倚相反。(8)也有证据表明碱基组成中的一些总体区域偏好可能影响密码子的使用。总的来说，这些结果表明，自然选择对果蝇属的密码子使用起了作用，至少经常足以在现代基因组中留下选择的足迹。然而，数据中有证据表明，随机力（漂移和突变）也在数据中留下了模式，特别是在密码子使用选择较弱的基因中，例如低重组区域的基因。这12个基因组中每个基因组的密码子使用模式的文档也有助于正在进行的注释工作。
Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined. The pattern of codon usage is generally similar among closely related species, but differs significantly among distantly related organisms, e.g., bacteria, yeast, and Drosophila. Several explanations for CUB have been offered and some have been supported by observations and experiments, although a thorough understanding of the evolutionary forces (random drift, mutation bias, and selection) and their relative importance remains to be determined. The recently available complete genome DNA sequences of twelve phylogenetically defined species of Drosophila offer a hitherto unprecedented opportunity to examine these problems. We report here the patterns of codon usage in the twelve species and offer insights on possible evolutionary forces involved. (1) Codon usage is quite stable across 11/12 of the species: G- and especially C-ending codons are used most frequently, thus defining the preferred codons. (2) The only amino acid that changes in preferred codon is Serine with six species of the melanogaster group favoring TCC while the other species, particularly subgenus Drosophila species, favor AGC. (3) D. willistoni is an exception to these generalizations in having a shifted codon usage for seven amino acids toward A/T in the wobble position. (4) Amino acids differ in their contribution to overall CUB, Leu having the greatest and Asp the least. (5) Among two-fold degenerate amino acids, A/G ending amino acids have more selection on codon usage than T/C ending amino acids. (6) Among the different chromosome arms or elements, genes on the non-recombining element F (dot chromosome) have the least CUB, while genes on the element A (X chromosome) have the most. (7) Introns indicate that mutation bias in all species is approximately 2:1, AT:GC, the opposite of codon usage bias. (8) There is also evidence for some overall regional bias in base composition that may influence codon usage. Overall, these results suggest that natural selection has acted on codon usage in the genus Drosophila, at least often enough to leave a footprint of selection in modern genomes. However, there is evidence in the data that random forces (drift and mutation) have also left patterns in the data, especially in genes under weak selection for codon usage for example genes in regions of low recombination. The documentation of codon usage patterns in each of these twelve genomes also aids in ongoing annotation efforts.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
DOI：
10.1017/s0016672302006067
发表时间：
2003-04-01
期刊：
GENETICAL RESEARCH
影响因子：
--
作者：
Kliman, RM;Hey, J
通讯作者：
Hey, J
DOI：
10.1073/pnas.212277199
发表时间：
2002-10-15
影响因子：
11.1
作者：
Betancourt, AJ;Presgraves, DC
通讯作者：
Presgraves, DC
影响因子：
1.5
作者：
Marais, G;Mouchiroud, D;Duret, L
通讯作者：
Duret, L